I think I remember reading that you can get a retro-fit Defiant that can cloak when you make Vice Admiral. It's all part of the Season 2 upgrades. I think one of the other ones was a retrofit to the Galaxy Class type ships that would allow Saucer separation, making your primary hull a Tatical Cruiser and your saucer section a 'pet' vessel. For the Science types, you are supposed to able to make and Intrepid type ship (aka Voyager) be able to get that armor that the Voyager had at the end of the series